Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

What's a virus, anyway? The bare-bones basics

scopeblog.stanford.edu

Post reply on HN
Print view View original

131–140 of 202 posts

Re: What's a virus, anyway? The bare-bones basics

#131

Post by __blockcipher__ »

Retric wrote: post #98
vikramkr wrote: post #70

Earlier quoted context omitted.

Edit - I'll concede that analogies are absolutely fun haha. They might be useful to come up with when you yourself are trying to better understand something by drawing connections to other things you know and all. But I don't think they're ideal for being taught the subject. And again, for a layperson, analogies are totally fine if you just want a surface level understanding of "oh, mitochondrias are powerhouses of t…

The problem with including codons in such a high level analogy of DNA is their context sensitive. DNA doesn’t care about those details and can be sliced an diced to completely change how it’s interpreted. Also, you really should include activation sites etc, but soon your out of the realms of analogy and just describing the details.

The big component missing in the analogy is gene expression. That’s what makes DNA behave differently from simple instruction mappings.

I guess we could visualize it as a series of drains, where the size of the hole can be modulated. Since gene expression can decrease or increase the rate at which DNA is transcribed

Re: What's a virus, anyway? The bare-bones basics

#132

Post by SirLuxuryYacht »

guscost wrote: post #117
twomoretime wrote: post #39

Earlier quoted context omitted.

It's like writing ultimate spaghetti code in a dynamic language. The nature of biology is much like classes and data floating around and all seemingly randomly interacting with each other, because ultimately this is just chemistry with thousands of unique compounds, which makes things messy. But through natural selection it seems to work. Like a totally incomprehensible compression algorithm learned by neural nets or…

And not only is it far worse than the most spaghettified and surprising program/meta-program you've ever seen, it's also a quine .

For those like me:

https://en.wikipedia.org/wiki/Quine_(computing)

Re: What's a virus, anyway? The bare-bones basics

#133

Post by ksk »

lawrenceyan wrote: post #3

In the case of the coronavirus, we see a significant binding affinity to the ACE2 membrane protein, which explains why the infection targets the lungs and guts so readily.

I believe it has been known for about 15 years now, that ACE2 positive epithelial cells are a potential vector for the coronavirus family of viruses.

I think with SARS-CoV-2 the pathogenesis is still not properly understood. For e.g. if you take a look at the ACE-2 expressing cell distribution, the tongue and oral cavity are very high on the list. And yet, there is no current guidance on disinfecting food before eating it, even though its a potentially high-risk route of infection.

https://www.ncbi.nlm.nih.gov/pubmed/16690935

Re: What's a virus, anyway? The bare-bones basics

#134

Post by ses1984 »

dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

This doesn't exactly answer the question but if you haven't read the selfish gene, you should.

Re: What's a virus, anyway? The bare-bones basics

#135

Post by ses1984 »

ufo wrote: post #64
dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

The cliff notes version of it is that DNA encodes the information on how to build proteins. https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio... Proteins are built out of a chain of aminoacids. There are 20 different kinds of aminoacid, and the particular sequence of aminoacids determines the shape of the protein, and therefore its biological function. https://en.wikipedia.org/wiki/Amino_acid To build a pr…

Why do cells replicate virus rns so much, why don't we replicate out own rna out of control by the same mechanism?

Re: What's a virus, anyway? The bare-bones basics

#136

Post by mjfl »

dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

The cell is an analog computer, but one who's computational state we are still working out describing (it consists of the concentrations of transcription factors as well as epigenetic modifications of DNA and chromatin), and who's evolution in time is governed by simple binding and enzyme kinetics, but that are integrated into networks that can be very complicated.

One really simplified model (inaccurate, but useful) of the computational state and evolution of the cell involves DNA methylation. DNA is methylated to shut it off, demethylation turns it on. To turn some DNA off or on, either DNA methyltransferase (DNMT3a/b) for methylation or one of the Tet proteins for demethylation needs to be guided to that region of DNA, usually through the assembly of some transcription factor complexes. The assembly of these complexes is combinatorial and performs logical addressing depending on the cell state. For example the cell may be expressing TF's A, B, and C, and these guide DNMT3a/b to DNA locus 3xq3945 (made up, whatever) if beta catenin translocates to the nucleus as a response to Wnt signaling, to turn something off. If TF's A, B, and D are expressed, it may bring it to a different location, and may bring Tet there instead, for demethylation.

Anyways, that's an example of "computery" description of cell biology. I don't really like how other responders shot your question down, I think the computer science mindset is really relevant to biology.

Re: What's a virus, anyway? The bare-bones basics

#137

Post by lordnacho »

smaddox wrote: post #56
lordnacho wrote: post #30

Earlier quoted context omitted.

I listened to the Great Courses audiobook about Biology. There's a lot about how the machinery of the cell works, how it evolved, and so on. He goes through everything else as well, including the immune system, ecology, and so on. It all ties together. Regarding the genes and central dogma, he gives a LOT of detail about how for instance it was discovered that codons work in threes (not twos or fours). Also how it wa…

Do you have a link to it on Audible, or somewhere? There seem to be several Great Courses on Biology. I absolutely love the series, and the one you're describing definitely sounds like one I would like to listen to.

Think the guys name was Nowicki

Re: What's a virus, anyway? The bare-bones basics

#138

Post by usrusr »

titzer wrote: post #100
ggm wrote: post #94

Wise words a former cell biology aware PhD said to me once: a cell is at a scale where van der Waals forces means 'water' isn't behaving like you think and the 'liquid' of a cell is possibly more like a matrix than a fluid. Those high school cell models are very misleading. He basically said macro scale intuition was useless for what it means to pierce the cell wall, as an example. What does "pierce" even mean?

Agree! I found ( https://blogs.scientificamerican.com/observations/watch-the-... ) to be pretty mind-blowing.

Un-narrated version, for those who were taken by the music: https://vimeo.com/260291601

Re: What's a virus, anyway? The bare-bones basics

#139

Post by matheusmoreira »

dimtion wrote: post #25

Is there a a good read on how RNA and DNA work for a Computer Scientist? And more generally how biology, genetics, epigenetics, virus, etc work? Many vulgarization sources say that DNA is like the source code of life. But they mostly skim across the issue and go to conclusions like "this gene or set of genes are responsible for that outcome". But coming from a CS background that sounds a bit like non-sense. I feel li…

> Is there a a good read on how RNA and DNA work for a Computer Scientist?

DNA is source code. RNA is an intermediate representation. Enzymes compile DNA into mRNA. Ribosomes compile mRNA into proteins which can actually execute a wide variety of functions.

Proteins may require post-processing before they're usable. The output of a ribosome is a primary protein: a linear, one-dimensional structure. By interacting with itself and other cell machinery, the protein could be folded into three-dimensional secondary and tertiary structures. Several of them might be assembled into a quaternary protein.

https://en.wikipedia.org/wiki/Protein_structure

The final result could be a simple peptide or some huge machine like this thing:

https://en.wikipedia.org/wiki/Type_three_secretion_system

The mitochondrion and the ATP synthase are like a hydroelectric power plant. The electrochemical gradient is the gravity, the hydrogen is the water and the enzyme is the turbine.

https://en.wikipedia.org/wiki/ATP_synthase

Enzymes transform substrate into product. They're like functions. When one enzyme's product is another's substrate, a pipeline is formed. Metabolism is a parallel process. I've written about metabolism as a programming metaphor before:

https://news.ycombinator.com/item?id=21562716

Sometimes bacteria save useful snippets of their own source code into gene cassettes. This allows the code to be exported to other bacteria via horizontal gene transfer.

https://en.wikipedia.org/wiki/Gene_cassette

Developed an awesome antibiotic-destroying enzyme? Make copies and send them to friends through a pipe. Didn't manage to survive? Said friends might be able to absorb the DNA from the environment anyway. They can obtain the fallen's powers just like Mega Man.

Re: What's a virus, anyway? The bare-bones basics

#140

Post by usrusr »

johnohara wrote: post #111
titzer wrote: post #100

Earlier quoted context omitted.

Agree! I found ( https://blogs.scientificamerican.com/observations/watch-the-... ) to be pretty mind-blowing.

Pity I only get 1 upvote. I'd triple-click if I could. This animation enables one to visualize a single SARS-CoV-2 virion binding with the ACE2 enzyme, entering the host cell, and replicating 4-5 new virions. One SARS-CoV-2 virion is 125 nanometers wide. By the time it shows up on a CT scan we are talking many, many billions. It's seems impossible anyone could test positive and still be asymptomatic.

> It's seems impossible anyone could test positive and still be asymptomatic.

Why? Most symptoms are part of the body's response switching into overdrive and not a direct consequence of cells getting subverted into virion farms. If the immune system wins without resorting to state of emergency measures like a fever you won't notice, but in the meantime there is a phase of viral replication in the throat.

With SARS-Cov-2 there is even the pattern that detection drops already in the throat of patients that still have a pneumonia raging in their lung (probably because the throat, as a battlefield in this war, somehow favors the immune system more than the lung?), so it's not even a subset/superset relation between symptoms and positive throat PCR, it's a partial overlap.

Post reply on HN